org.strbio.local
Class PDB
java.lang.Object
org.strbio.local.PDB
public class PDB
- extends java.lang.Object
Class to access a local copy of the PDB. Classes to read PDB or
DSSP files as Proteins are found in ProteinSet.
Version 1.2, 11/14/02 - added support for SCOP-style names
Version 1.1, 7/28/99 - adapted to new PDBInfo structure
Version 1.0, 7/22/99 - original version
- Version:
- 1.2, 11/14/02
- Author:
- JMC
- See Also:
ProteinSet
Field Summary |
static java.lang.String |
DEFAULT_PDB_PATH
The default PDB path for all users of this library. |
Constructor Summary |
PDB()
|
Method Summary |
static java.lang.String |
findPDBName(java.lang.String name,
Printf outfile)
Find PDB file corresponding to a given protein name. |
static PDBInfo |
getInfo(java.lang.String name,
Printf outfile)
Gets info on a PDB file for a given PDB code. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DEFAULT_PDB_PATH
public static final java.lang.String DEFAULT_PDB_PATH
- The default PDB path for all users of this library. This
is system-dependent.
- See Also:
- Constant Field Values
PDB
public PDB()
findPDBName
public static final java.lang.String findPDBName(java.lang.String name,
Printf outfile)
- Find PDB file corresponding to a given protein name. Looks
for a property called pdb.path in ~/.pdb.properties. If this
is not found, it uses the default pdb path. This is a colon or
semicolon separated
string listing directories you want to look for PDB files.
Each of these directories can have subdirectories with proteins
sorted by the first letter or first 2 letters of the PDB code.
The order of searching each directory is as follows:
- exact name (i.e. 1abc)
- name with .pdb appended to it (1abc -> 1abc.pdb)
- 1abc or 1ABC -> pdb1abc.ent
- 1abc or 1ABC -> ab/pdb1abc.ent
- 1abc or 1ABC -> a/pdb1abc.ent
- All of above, with first character truncated, i.e. d2minb_ treated like 2min
Also, all combinations ending in .gz are checked.
getInfo
public static final PDBInfo getInfo(java.lang.String name,
Printf outfile)
- Gets info on a PDB file for a given PDB code.